Global Death Rates of Different Types of Cancers, 1990-2019

Project Background and Data

Project Aim and Research Question

This project aimed to investigate changes in the death rate (per 100,000 people) for multiple different types of cancer globally.

Specifically, it aimed to visualise any dramatic changes or trends in these death rates. As a result of this original visualisation, a further two visualisations were produced in order to investigate whether or not these trends that were found changed significantly when looking at just the male or female figures.

Data Origins

The data used in this project was taken from The Global Burden of Disease Study (2019), collected by The Institute for Health Metrics and Evaluation. From this I was able to download data on the global death rates of every type of cancer between 1990-2019 for both sexes.

Project Organisation

I created three different scripts for each visualisation for better organisation. All of the outputs are saved in the figs folder, and the raw data is saved in the data folder. There is also a codebook included that details the variables used in the datasets.

Data Preparation

Loading Packages

This project has used the renv package in order to ensure anybody running this project will use the same versions of the packages.

#load the renv package
install.packages ("renv")
library(renv)
renv::snapshot()
#restore the project environment 
renv::restore()

#load other packages
library(here) #for setting working directory
library(tidyverse) #for data preparation
library(dplyr) #for data manipulation
library(ggplot2) #to make graphs
library(plotly) #to make interactive graphs
library(ggtext) #for formatting labels

Importing the data

#load data needed for all 3 visualisations
all_data <- read.csv(here("DATA", "cancer_data.csv"))
female_data <- read.csv(here("DATA", "female_data.csv"))
male_data <- read.csv(here( "DATA", "male_data.csv"))

The first 5 rows of the first dataset displayed in order to check it imported correctly

#Print the first few rows of data
print(head(all_data))

##   measure location  sex      age             cause metric year       val
## 1  Deaths   Global Both All ages Testicular cancer   Rate 2006 0.1287813
## 2  Deaths   Global Both All ages Testicular cancer   Rate 2007 0.1288621
## 3  Deaths   Global Both All ages Testicular cancer   Rate 2005 0.1291316
## 4  Deaths   Global Both All ages Testicular cancer   Rate 2004 0.1293314
## 5  Deaths   Global Both All ages Testicular cancer   Rate 2003 0.1294418
## 6  Deaths   Global Both All ages Testicular cancer   Rate 2008 0.1294725
##       upper     lower
## 1 0.1416675 0.1222793
## 2 0.1416227 0.1225175
## 3 0.1422235 0.1223017
## 4 0.1412705 0.1228608
## 5 0.1416219 0.1225994
## 6 0.1433455 0.1228090

Data Wrangling

# Remove certain columns from each dataset as these are not needed
new_all_data <- all_data%>%
  select(-upper, -lower, - age, - sex, -location, -metric)

new_female_data <- female_data%>%
  select(-measure_id, -measure_name, -location_id, -location_name, -sex_id, -sex_name
         , -age_id, -age_name, -cause_id, -metric_id, -metric_name, -upper, -lower) 

new_male_data <- male_data%>%
  select(-measure_id, -measure_name, -location_id, -location_name, -sex_id, -sex_name
         , -age_id, -age_name, -cause_id, -metric_id, -metric_name, -upper, -lower)


#rename columns and remove rows that are not needed
#For my first visualisation I removed 19 of the 30 cancers included in the original dataset in order to make the visualisation both more relevant and easier to read
#I determined this by removing any cancer that had a death rate for all years of under 3.3

new_all_data <- new_all_data %>%
  rename(Cancer_Type = cause, Year = year, Death_Rate = val)

new_female_data <- new_female_data %>%
  rename(Cancer_Type = cause_name, Year = year, Death_Rate = val)

new_male_data <- new_male_data %>%
  rename(Cancer_Type = cause_name, Year = year, Death_Rate = val)

new_all_data <- subset(new_all_data, 
                       Cancer_Type != "Other neoplasms" &
                         Cancer_Type != "Hodgkin lymphoma" &
                         Cancer_Type != "Mesothelioma" &
                         Cancer_Type != "Testicular cancer" &
                         Cancer_Type != "Malignant skin melanoma" &
                         Cancer_Type != "Other pharynx cancer" &
                         Cancer_Type != "Larynx cancer" &
                         Cancer_Type != "Multiple myeloma" &
                         Cancer_Type != "Nasopharynx cancer" &
                         Cancer_Type != "Thyroid cancer" &
                         Cancer_Type != "Non-melanoma skin cancer" &
                         Cancer_Type != "Uterine cancer" &
                         Cancer_Type != "Kidney cancer" &
                         Cancer_Type != "Gallbladder and biliary tract cancer"&
                         Cancer_Type != "Lip and oral cavity cancer"&
                         Cancer_Type != "Ovarian cancer"&
                         Cancer_Type != "Bladder cancer"&
                         Cancer_Type != "Non-Hodgkin lymphoma"&
                         Cancer_Type != "Brain and central nervous system cancer")


#for visualisations 2 and 3 I removed an extra 9 cancers in order to only focus on the 3 I wanted to look at
#I used a transformation function so that I could apply it to both the female and male datasets 

transform_data <- function(data) {data <- data %>%
  filter(
                         Cancer_Type != "Other neoplasms" &
                         Cancer_Type != "Hodgkin lymphoma" &
                         Cancer_Type != "Mesothelioma" &
                         Cancer_Type != "Testicular cancer" &
                         Cancer_Type != "Malignant skin melanoma" &
                         Cancer_Type != "Other pharynx cancer" &
                         Cancer_Type != "Larynx cancer" &
                         Cancer_Type != "Multiple myeloma" &
                         Cancer_Type != "Nasopharynx cancer" &
                         Cancer_Type != "Thyroid cancer" &
                         Cancer_Type != "Non-melanoma skin cancer" &
                         Cancer_Type != "Uterine cancer" &
                         Cancer_Type != "Kidney cancer" &
                         Cancer_Type != "Gallbladder and biliary tract cancer"&
                         Cancer_Type != "Lip and oral cavity cancer"&
                         Cancer_Type != "Ovarian cancer"&
                         Cancer_Type != "Bladder cancer"&
                         Cancer_Type != "Non-Hodgkin lymphoma"&
                         Cancer_Type != "Brain and central nervous system cancer"&
                         Cancer_Type != "Pancreatic cancer"&
                         Cancer_Type != "Cervical cancer"&
                         Cancer_Type != "Leukemia"&
                         Cancer_Type != "Prostate cancer"&
                         Cancer_Type != "Other malignant neoplasms"&
                         Cancer_Type != "Liver cancer"&
                         Cancer_Type != "Esophageal cancer"&
                         Cancer_Type != "Breast cancer")
                        
        
return(data)
}


#apply the transformation function to both the datasets 
new_female_data <- transform_data(new_female_data)
new_male_data <- transform_data(new_male_data)

Visualisations

Visualisation 1

For my first visualisation I used the first dataset which contained the death rates for 12 different types of cancer between 1990-2019 for both of the sexes.

This allowed me to visualise any dramatic changes in these death rates across the 30 year period.

#factor the variable "Cancer Type" in order to create defined levels 
new_all_data$Cancer_Type <- factor(new_all_data$Cancer_Type)

# Change levels of Cancer_Type Variable
new_all_data$Cancer_Type <- factor(new_all_data$Cancer_Type, levels = unique(new_all_data$Cancer_Type))

#plot a standard line graph
#add appropriate title and labels
p <- ggplot(new_all_data, aes(x = Year, y = Death_Rate, color = Cancer_Type)) + 
  geom_line() + labs(
    x = "Year", 
    y = "Death Rate (Per 100,000)", 
    color = "Cancer Type",
    title ="Changing Death Rates of Different Types of Cancer: 1990-2019\n<span style='font-size: 12; font-style: italic'>Institute for Health Metrics and Evaluation</span>") + 
  scale_y_continuous(breaks = seq(0, 35, by = 5), labels = seq(0, 35, by = 5)) +
  theme_minimal() 

#Change the aesthetics (font, font size, position) of the title, legend and labels
p <- p +
  theme(
    text = element_text(family = "helvetica"),
    legend.text = element_text(size = 9),
    legend.title = element_text(face = "bold", size = 15),
    plot.title = element_text(size = 13, face = "bold",  hjust = 0.5, vjust = 1),
    axis.title.x = element_text(face = "bold", size = 12), 
    axis.title.y = element_text(face = "bold", size = 12)
  )


#change the colour of the plot lines  
colours <- c("red","brown", "cornflowerblue","chartreuse2", "orange", "black","darkred","lightblue",
             "darkblue", "darkgreen","hotpink", "purple")

p <- p + scale_color_manual(values = colours) 

# Make the line graph interactive and specify the width using the plotly package
ip <- ggplotly(p, width = 1000, height = 700, tooltip =  c("Year", "Death_Rate", "Cancer_Type"),
               labels = c("Year", "Death Rate", "Cancer Type"))


ip

The final output is saved in the ‘figs’ folder

# Save interactive plot as an html
htmlwidgets::saveWidget(ip, file = "../figs/All_Cancer_Deaths.html")

blah blah blah this gave me more questions, lead onto visualisation 2 and 3

Visualisation 2

#factor the variable "Cancer Type" in order to create defined levels 
new_female_data$Cancer_Type <- factor(new_female_data$Cancer_Type)

# Change levels of Cancer_Type Variable
new_female_data$Cancer_Type <- factor(new_female_data$Cancer_Type, levels = unique(new_female_data$Cancer_Type))

#plot a standard line graph
#add appropriate title and labels
p <- ggplot(new_female_data, aes(x = Year, y = Death_Rate, color = Cancer_Type)) + 
  geom_line() + labs(
    x = "Year", 
    y = "Death Rate (Per 100,000)", 
    color = "Cancer Type",
    title ="Changing Death Rates of Different Types of Cancer in Females: 1990-2019\n<span style='font-size: 12; font-style: italic'>Institute for Health Metrics and Evaluation</span>") + 
  scale_y_continuous(breaks = seq(0, 35, by = 5), labels = seq(0, 35, by = 5)) +
  theme_minimal() 

#Change the aesthetics (font, font size, position) of the title, legend and labels
p <- p +
  theme(
    text = element_text(family = "helvetica"),
    legend.text = element_text(size = 9),
    legend.title = element_text(face = "bold", size = 15),
    plot.title = element_text(size = 13, face = "bold",  hjust = 0.5, vjust = 1),
    axis.title.x = element_text(face = "bold", size = 12), 
    axis.title.y = element_text(face = "bold", size = 12)
  )


# Define custom colors for each cancer type in order to match the colours of visualisation 1
custom_colours <- c("Stomach cancer" = "darkgreen", "Tracheal, bronchus, and lung cancer" = "hotpink", "Colon and rectum cancer" = "darkblue")
                   


p <- p + scale_color_manual(values = custom_colours) 

# Make the line graph interactive and specify the width using the plotly package
ip <- ggplotly(p, width = 1000, height = 700, tooltip =  c("Year", "Death_Rate", "Cancer_Type"),
               labels = c("Year", "Death Rate", "Cancer Type"))


ip

The final output is saved in the ‘figs’ folder

# Save interactive plot as an html
htmlwidgets::saveWidget(ip, file = "../figs/Female_Cancer_Deaths.html")

#factor the variable "Cancer Type" in order to create defined levels 
new_male_data$Cancer_Type <- factor(new_male_data$Cancer_Type)

# Change levels of Cancer_Type Variable
new_male_data$Cancer_Type <- factor(new_male_data$Cancer_Type, levels = unique(new_male_data$Cancer_Type))

#plot a standard line graph
#add appropriate title and labels
p <- ggplot(new_male_data, aes(x = Year, y = Death_Rate, color = Cancer_Type)) + 
  geom_line() + labs(
    x = "Year", 
    y = "Death Rate (Per 100,000)", 
    color = "Cancer Type",
    title ="Changing Death Rates of Different Types of Cancer in Males: 1990-2019\n<span style='font-size: 12; font-style: italic'>Institute for Health Metrics and Evaluation</span>") + 
  scale_y_continuous(breaks = seq(0, 35, by = 5), labels = seq(0, 35, by = 5)) +
  theme_minimal() 

#Change the aesthetics (font, font size, position) of the title, legend and labels
p <- p +
  theme(
    text = element_text(family = "helvetica"),
    legend.text = element_text(size = 9),
    legend.title = element_text(face = "bold", size = 15),
    plot.title = element_text(size = 13, face = "bold",  hjust = 0.5, vjust = 1),
    axis.title.x = element_text(face = "bold", size = 12), 
    axis.title.y = element_text(face = "bold", size = 12)
  )


# Define custom colors for each cancer type in order to match the colours of visualisation 1
custom_colours <- c("Stomach cancer" = "darkgreen", "Tracheal, bronchus, and lung cancer" = "hotpink", "Colon and rectum cancer" = "darkblue")
                  

p <- p + scale_color_manual(values = custom_colours) 

# Make the line graph interactive and specify the width using the plotly package
ip <- ggplotly(p, width = 1000, height = 700, tooltip =  c("Year", "Death_Rate", "Cancer_Type"),
               labels = c("Year", "Death Rate", "Cancer Type"))


ip

The final output is saved in the ‘figs’ folder

# Save interactive plot as an html
htmlwidgets::saveWidget(ip, file = "../figs/Male_Cancer_Deaths.html")

Interpretations

References